Table 1: List of aptamers grouped by organism and type categories, with number of aptamers per category shown in right-most column.
| Organism | Type | Aptamer_Count |
|---|---|---|
| Human | Protein | 7289 |
| Mouse | Protein | 233 |
| Human | Spuriomer | 20 |
| Human | Hybridization Control Elution | 12 |
| Human | Non-Biotin | 10 |
| Human | Non-Cleavable | 4 |
| African clawed frog | Non-Human | 3 |
| Gila monster | Non-Human | 3 |
| Hornet | Non-Human | 3 |
| Jellyfish | Non-Human | 3 |
| Mouse | Non-Human | 3 |
| Thermus thermophilus | Non-Human | 3 |
| Common eastern firefly | Non-Human | 2 |
| European elder | Non-Human | 2 |
| Bacillus stearothermophilus | Non-Human | 1 |
| Ensifer meliloti | Non-Human | 1 |
| HIV-1 | Protein | 1 |
| HIV-2 | Protein | 1 |
| Red alga|Red alga | Non-Human | 1 |
| strain K12 | Non-Human | 1 |
Table 2: Number of human protein aptamers (7289, see Table 1) per quality category. Quality refers to the success with which the human protein-designed aptamer is able to quantify protein intensity in mouse plasma samples.
| Quality | Count |
|---|---|
| High | 2653 |
| Low | 910 |
| Medium | 3726 |
Figure 1: Plots of aptamer counts per sample for A) mouse and B) human datasets above eLoD calculated for each aptamer (eLoD = Median_blank + 4.9MAD_blank). Blue horizontal line indicate the total number of aptamers in the panel (7596). Red horizontal line (mouse only) indicates the number of human protein aptamers assessed to perform with high/medium quality in mouse samples.
Figure 2: Plots of aptamer counts per sample for A) mouse and B) human pre-normalization datasets above eLoD calculated for each aptamer (eLoD = Median_blank + 4.9MAD_blank). Blue horizontal line indicate the total number of aptamers in the panel (7596). Red horizontal line (mouse only) indicates the number of human protein aptamers assessed to perform with high/medium quality in mouse samples.
Figure 3: Boxplots showing distribution of aptamer intensities by sample for mouse and human datasets, final data and pre-normalization data for each. Plots are color coded by clinical group for both datasets. Most samples in each dataset have similar intensity distributions. Calibrator samples and hemolysis samples (mouse only) show slightly wider distribution ranges. The sole AK mouse sample has a slightly lower-shifted distribution compared to other samples.
Figure X: Bar graph showing number of aptamers removed by eLoD filter per sample for mouse datasets.
Figure X: Boxplots showing distribution of removed aptamer counts per sample, grouped by aptamer quality in mouse. Outliers - samples with an irregular number of aptamers removed - are labeled.
Figure X: Bar graph showing number of aptamers removed by eLoD filter per sample for human datasets.
Figure X: Bar graph showing distribution of aptamers removed using eLoD filter, categorized by aptamer quality score in mouse system.
Figure X: Scatter plot showing the intensity distribution for three aptamers: seq.10000.28 (high quality aptamer in mouse), seq.10044.12 (low quality), and seq.10003.15 (medium quality). The low quality aptamer has higher variation then both the medium and high quality aptamers in both the normalized and pre-normalization mouse datasets, although the difference is more apparent in the normalized dataset.
Figure 4: P-value distributions for the wilcox tests performed on the mouse dilution series data (pre-normalization).
Figure 5: Volcano plots showing significantly differentially expressed proteins between mouse dilution series samples A) 35uL vs. 55uL, B) 35uL vs. 55uL Diluted [35uL sample, 20uL PBS], C) 55uL vs. 55uL Diluted.
Table X: Number of aptamers/proteins detected per mouse dilution series sample (pre-normalization). The 55uL Diluted samples have the lowest counts, but all are decently high (max 7596 aptamers).
| Category | Sample_ID | AptCount |
|---|---|---|
| 35uL | Mouse 35 uL Rep 1 | 7512 |
| 35uL | Mouse 35 uL Rep 2 | 7534 |
| 35uL | Mouse 35 uL Rep 3 | 7540 |
| 55uL | Mouse A Series Rep 1 | 7537 |
| 55uL | Mouse A Series Rep 2 | 7537 |
| 55uL | Mouse A Series Rep 3 | 7550 |
| 55uL Diluted | Mouse B Series Rep 1 | 7491 |
| 55uL Diluted | Mouse B Series Rep 2 | 7403 |
| 55uL Diluted | Mouse B Series Rep 3 | 7421 |
Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between aptamers in the Hemolysis and Pooled 55uL groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure X: Volcano plots showing significantly differentially expressed proteins between hemolysis and pooled 55uL groups in mouse data, A) normalized, B) pre-normalization.
| Table_Key | Aptamer_Target | Target_Full_Name |
|---|---|---|
| 1 | seq.17137.160_Beta-globin | Hemoglobin subunit beta |
| 2 | seq.18198.51_HBAT | Hemoglobin subunit theta-1 |
| 3 | seq.19774.8_HBG2 | Hemoglobin subunit gamma-2 |
| 4 | seq.4915.64_Hemoglobin | Hemoglobin |
| 5 | seq.6919.3_HBAZ | Hemoglobin subunit zeta |
| 6 | seq.6992.67_HBD | Hemoglobin subunit delta |
| 7 | seq.7136.107_Hemoglobin epsilon chain | Hemoglobin subunit epsilon |
| 8 | seq.7965.25_HBAT | Hemoglobin subunit theta-1 |
| 9 | seq.9025.5_AHSP | Alpha-hemoglobin-stabilizing protein |
| Table_Key | Aptamer_Target | Target_Full_Name |
|---|---|---|
| 1 | seq.3054.3_Haptoglobin, Mixed Type | Haptoglobin |
| 2 | seq.7905.30_HPT | Haptoglobin isoform 2 |
Reveals differentially abundant proteins in autochthonous PDAC model
Figure X: P-value distributions for the wilcox tests performed on the mouse data comparing intensity (RFU) values between aptamers in the KMC-PDAC and Healthy Control - Late/KP Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure X: Volcano plots showing significantly differentially expressed proteins between KMC - PDAC and Healthy Control - Late/KP Late groups in mouse data, A) normalized, B) pre-normalization.
Reveals differentially abundant proteins in autochthonous lung cancer model
Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the KPC-Lung and KP Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure X: Volcano plots showing significantly differentially expressed proteins between KPC-Lung and Healthy Control - Late/KP Late groups in mouse data, A) normalized, B) pre-normalization.
Reveals differentially abundant proteins in autochthonous Myc-driven PDAC model
Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the KMC-PDAC and KMC Control groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure X: Volcano plots showing significantly differentially expressed proteins between KMC-PDAC and KMC Control groups in mouse data, A) normalized, B) pre-normalization.
Figure X: P-value distributions for the t-tests performed on the mouse data comparing intensity (RFU) values between proteins in the KMC-PDAC and KMC Control groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure X: Volcano plots of t-test results showing significantly differentially expressed proteins between KMC-PDAC and KMC Control groups in mouse data, A) normalized, B) pre-normalization.
Reveals differentially abundant proteins in early lethal PanIN model
Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the KPC - Early and Healthy control - early/KP-early groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure X: Volcano plots showing significantly differentially expressed proteins between KPC - early and Healthy control - early/KP - early groups in mouse data, A) normalized, B) pre-normalization.
Reveals differentially abundant proteins in late lethal PanIN model
Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the Lethal PanIN - Late/KPC - Late and Healthy Control - Late/KP-Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure X: Volcano plots showing significantly differentially expressed proteins between Lethal PanIN - Late/KPC - Late and Healthy Control - Late/KP-Late groups in mouse data, A) normalized, B) pre-normalization.
Reveals differentially abundant proteins in non-lethal PanIN model
Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the Non-lethal PanIN - Late/KC - Late and Healthy Control - Late/KP-Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure X: Volcano plots showing significantly differentially expressed proteins between Non-lethal PanIN - Late/KC - Late and Healthy Control - Late/KP-Late groups in mouse data, A) normalized, B) pre-normalization.
Figure 6: P-value distributions for the wilcox tests performed on the human dilution series data (pre-normalization).
Figure 7: Volcano plots showing significantly differentially expressed proteins between human dilution series samples A) 35uL vs. 55uL, B) 35uL vs. 55uL Diluted [35uL sample, 20uL PBS], C) 55uL vs. 55uL Diluted.
Table X: Number of aptamers/proteins detected per human dilution series sample (pre-normalization). The 55uL Diluted samples have the lowest counts, but all are decently high (max 7596 aptamers).
| Category | Sample_ID | AptCount |
|---|---|---|
| 35uL | Human 35 uL Rep 1 | 7553 |
| 35uL | Human 35 uL Rep 2 | 7558 |
| 35uL | Human 35 uL Rep 3 | 7561 |
| 55uL | Human A Series Rep 1 | 7566 |
| 55uL | Human A Series Rep 2 | 7576 |
| 55uL | Human A Series Rep 3 | 7577 |
| 55uL Diluted | Human B Series Rep 1 | 7503 |
| 55uL Diluted | Human B Series Rep 2 | 7482 |
| 55uL Diluted | Human B Series Rep 3 | 7504 |
Figure X: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and All Controls groups. A) Normalized human data, B) Pre-normalization human data.
Figure X: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and All Controls groups in human data, A) normalized, B) pre-normalization.
Figure X: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and Control (Benign) groups. A) Normalized human data, B) Pre-normalization human data.
Figure X: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and Control (Benign) groups in human data, A) normalized, B) pre-normalization.
Figure X: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and Control (Benign Prostatic Hyperplasia) groups. A) Normalized human data, B) Pre-normalization human data.
Figure X: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and Control (Benign Prostatic Hyperplasia) groups in human data, A) normalized, B) pre-normalization.
Figure X: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and Control (Prostatic Intraepithelial Neoplasia) groups. A) Normalized human data, B) Pre-normalization human data.
Figure X: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and Control (Prostatic Intraepithelial Neoplasia) groups in human data, A) normalized, B) pre-normalization.